How Digestion and the Gut Microbiome Work

The digestive system in plain terms

The digestive system is the tube that runs from your mouth to your anus (the stomach, small intestine and large intestine are its main parts), plus the liver, pancreas and gallbladder that add digestive juices. [1] Its job is to break food into pieces small enough to absorb and use for energy, growth and repair. [1]

Food is pushed along by waves of muscle movement called peristalsis. In the large intestine, water is absorbed and the waste that remains becomes stool. [1] Chewing, stomach acid, bile and enzymes all help along the way. Nerves and hormones help control the whole process. [1]

What is the gut microbiome?

Your large intestine contains a large number of bacteria and some fungi and viruses that make up the gut microbiome. [2] These microbes help with digestion. [1] For example, bacteria in the large intestine break down carbohydrates that the stomach and small intestine do not fully digest, and gas is made in the process. [2]

That is why gas is a normal part of digestion, and why eating more of certain fermentable carbohydrates can mean more gas. See bloating and gas. For plain definitions of probiotics, prebiotics and fermented foods, see probiotics, prebiotics and fermented foods.

The gut and brain talk to each other

Nerves and hormones help control digestion. [1] Many long-lasting digestive conditions, including IBS, are now called disorders of gut-brain interaction. They are related to problems with how the brain and gut work together, which can make the gut more sensitive and change how its muscles contract. [3]

This does not mean symptoms are "in your head." Pain, bloating and bowel changes are real. In IBS, for example, some people feel pain when a normal amount of gas or stool is in the gut. [4] Doctors may suggest mental health therapies for IBS, such as cognitive behavioral therapy, gut-directed hypnotherapy or relaxation training. [5] A US guideline also suggests gut-directed psychotherapy for global IBS symptoms. [6] For stress-related tools, see how to relieve stress and breathing exercises for stress.

What research does and does not show about the microbiome

• Differences are documented in some diseases. Studies have found differences between the microbiomes of people with inflammatory bowel disease and those without, but researchers are still studying how the two are related. [7]
• Diet variety is a reasonable aim. NIDDK notes that eating a variety of healthy foods can improve healthy bacteria in the gut. [8] This is general advice, not proof that any specific food "fixes" a microbiome.
• Consumer microbiome tests are not ready for clinical use. An international expert consensus statement says evidence supporting the clinical usefulness of microbiome testing is scarce, and that direct-to-consumer tests have no consensus on regulation or proven value in practice. [9] See the claim check on gut tests.
• Probiotic supplements are not a general microbiome fix. NCCIH says that in most instances it is still not known which probiotics are helpful and which are not. [10] See probiotics and prebiotics for gut health.

Evidence label: for the statement that the microbiome plays a role in digestion, this is an established part of basic physiology. For using the microbiome to diagnose or treat everyday symptoms, the evidence is insufficient.

When to get help

Knowing how digestion works can help you describe symptoms, but it cannot tell you the cause. See a clinician for blood in stool, black and tarry stools, constant belly pain, repeated vomiting, or weight loss you did not intend. [11][12] Details: digestive symptoms: red flags.